I see conflicting information on whether or not Windex (or ammonia-based glass cleaners) is harmful for the windshield. For example, thoughtco claims:

In reality, auto shops and auto-glass replacement vendors report no
such problems with auto glass that has been cleaned routinely with
ordinary household glass cleaners containing ammonia. ...

While automobile windshield glass is constructed with a lamination
process that bonds separate layers to a vinyl center layer in order to
make the windshield shatter resistant, the outer surfaces are still
plain old-fashioned glass, and they can be cleaned just like any other
glass surfaces in your home. ...

To take the question further, we might also ask about what effect
ammonia-based glass cleaner will have on other surfaces. Very close to
the glass in your car windows there are rubber or vinyl seals, paint,
and chrome trim. And inside the car, you likely have leather, vinyl,
all sorts of plastics, and maybe even wood. Through long experience,
car care specialists have found that ammonia may hurt very, very old
paint jobs if they have already severely dried out. But even fairly
worn rubber and metal trim does not seem to suffer at all from the
contact with ammonia cleaners. Your windshield wipers, too, will
largely be unaffected by glass cleaners, unless they are already so
old they are on the verge of disintegration anyway.

Ammonia will harm WINDOW TINT, specifically, the plastic tint sheets installed by the dealer or other vendor. They use ammonia to remove old tint before installing new. Factory installed tint is part of the glass, not a plastic layer on the interior surface of the window. So, if you have non-factory tint don't use ammonia on it. If you don't have that tint, keep in mind the other cautions, damaging rubber and plastic, etc.
– Tim NevinsApr 23 at 20:51

Unless you're spraying on an ammonia-based cleaner and then using the windshield wipers to clean the glass, I don't see how it could harm the wipers. This would include using it in the wiper fluid tank.
– BillDOeApr 23 at 22:24